<p>Sow litter sizes have been increasing over the years. Increasing litter sizes typically result in an increased duration of farrowing which can be detrimental to piglet survival due to the increased risk of <i>in-utero</i> asphyxiation. The cumulative effect of repeated contractions over extended time results in increased pressure on the umbilical cord. This causes an interruption of blood and oxygen to the piglet brain, increasing the risk of death. Although asphyxiation is the cause of the majority of stillbirths, piglets who are born alive can also suffer from <i>in-utero</i> asphyxiation. These piglets are considered to be of low vitality and are severely disadvantaged in regard to survival and growth. Different methods have been explored on ways to decrease farrowing duration, reduce stillbirths, and improve piglet survival, but the neonatal mortality rate is still rather high and is not decreasing. Therefore, new methods need to be investigated in the hopes of successfully decreasing the farrowing duration of sows.</p> <p>The first project aimed to shorten the farrowing duration and improve piglet survival in farrowing crates via the provision of nesting material and enriched piglet mats. There have been several studies on the effects of nesting material in farrowing crates, but most of those studies use materials that will fall through the slatted floors and block the liquid manure systems. The current study implemented the use of jute as the nesting material and proposed a novel way to present the material, by attaching it to the side of the crate, to prevent it from falling through the slatted floors and disrupting the manure systems. The enriched piglet mats were made from a microfiber material to promote homeothermy and reduce heat loss, thus potentially positively impacting piglet growth and survival. Twenty sows were randomly assigned to 1 of 2 treatments: 1) farrowing crate with jute nesting material (Nest; n = 10; 3 pieces of jute, each 40.6 cm x 21.6 cm) and two enriched piglet mats made from an acrylic board (28.0 x 86.4 cm) covered with a microfiber material, or 2) farrowing crate without nesting material (Control; n = 10) and 1 standard rubber mat (28.0 x 86.4 cm) for piglets. Sows had access to the jute material from approximately d 113 of gestation until they finished farrowing, while piglets had access to the mats for the first 3 d of age. Sow saliva was collected to measure Immunoglobulin A (IgA) and cortisol to assess stress on d -1, 0, 1, and 2, relative to farrowing, and a final sample at weaning (d 16.9 ± 0.18). Piglet plasma Immunoglobulin G (IgG) was collected from 4 piglets/litter at 48 h, 7 d, and weaning. Piglet skin temperature was measured from two piglets/litter using an infrared camera for 3 d after birth. Video was continuously coded for observations of jute-directed and crate-directed interactions. Nest sows performed less crate-directed behavior than Control sows (<i>P</i> = 0.02), while both groups performed the same amount of total nesting behavior (the sum of crate-directed plus jute-directed behavior) (<i>P</i> > 0.05). Cortisol tended to be less in Nest sows (<i>P</i> = 0.08), but there was no difference in IgA concentrations (<i>P</i> > 0.4). Nest piglets tended to be heavier on d 7 (<i>P</i> = 0.095), had greater IgG concentrations (<i>P</i> = 0.03), and greater skin temperatures (P = 0.02). There were no differences in farrowing duration or number of stillbirths (<i>P</i> > 0.7). </p> <p>The second study investigated the effects of a dietary supplement, 6.6% resistant starch (RS), on sow farrowing performance and piglet survival and vitality. Since RS has been shown to help stabilize blood glucose levels post-prandially, it was hypothesized that RS would decrease farrowing duration by improving the energy status of sows during farrowing. Forty-two sows were balanced for parity and randomly assigned to 1 of 2 treatments: standard lactation diet (n = 21) or diet containing RS (n = 21). Sow blood was analyzed for glucose concentrations at baseline, after 1 wk of being on their respective diets, and during farrowing. Blood glucose for RS sows increased between the beginning and end of farrowing while Control sow blood glucose decreased (P = 0.04). However, there were no other effects on sow blood glucose. Farrowing duration and number of stillbirths did not differ between treatments (P > 0.05). Piglet blood glucose concentrations for RS piglets tended to increase as the birth order increased, while blood glucose for the Control piglets tended to decrease. The other piglet vitality measures, assessed by blood lactate, pH, partial pressure of carbon dioxide (PCO₂), partial pressure of oxygen (PO₂), total carbon dioxide (TCO₂), bicarbonate (HCO₃), base excess (BE_ecf), and oxygen saturation (sO₂) did not differ between treatments (<i>P</i> > 0.05).</p> <p>In conclusion, farrowing duration was not successfully decreased by the provision of jute nesting material attached to the side of the farrowing crate or by supplementation of RS. However, the jute nesting material and enriched piglet mats did positively impact sow welfare and piglet measures to an extent, although this did not translate into improved piglet survival. The resistant starch supplementation seemed to impact sow glucose during farrowing, but not enough to impact farrowing performance or piglet survival or vitality. These results could be because the nesting treatment was not robust enough to allow sows to fully express their nesting behavior needs in order to impact farrowing performance, while the RS supplementation may have been too low of a dosage, not fed long enough, or a less effective type of RS. Novel ways to optimize sow farrowing performance and piglet survival are still needed.</p>

A capivara é uma espécie da fauna silvestre que se favoreceu da situação de conversão de áreas florestais para fins agropecuários, tornando-se bastante comum. Tal superpopulação causa conflitos, especialmente em virtude de prejuízos agrícolas e riscos de transmissão de doenças. Entretanto, a espécie apresenta grande potencial zootécnico e econômico, sendo que, aparentemente, o sistema produtivo mais sustentável seria o extensivo. Para fornecer subsídios técnicos a este sistema, torna-se necessário o monitoramento das populações. Um dos métodos mais utilizados para populações de capivaras é o de contagem direta dos animais, utilizada usualmente em ambientes mais abertos, porém pouco eficiente em locais de vegetação mais fechada e para populações mais arredias. O que se buscou testar neste trabalho foi um método de monitoramento alternativo à contagem direta. O trabalho foi realizado em sete áreas, sendo quatro com populações fechadas e três abertas. Semanalmente foram contadas as fezes depositadas durante esse período numa área amostral, contados diretamente os animais e levantados dados sobre flutuação real das populações fechadas. A obtenção de um índice de abundância através da contagem de fezes apresentou um coeficiente de regressão linear melhor que a contagem direta, em comparação com a flutuação real da população, obtida em ambientes fechados. Porém, nenhum dos métodos apresentou resultados satisfatórios que refletissem, no índice, as alterações ocorridas na população. A contagem de fezes mostrou-se satisfatória para separar em faixas de número de indivíduos as diferentes populações e também na aplicação da estimativa populacional baseada na técnica de Índice-manipulação-índice. O trabalho levanta inúmeras questões a respeito da intensidade amostral, de possíveis estudos quanto ao uso do habitat e do grau de confiabilidade dos monitoramentos baseados em contagens diretas. / The capybara is a wild species that would be favored by the conversion of the forest areas to farmlands, becoming abundant. Such overpopulation causes conflicts, especially due to agricultural damages and risks of transmission of illnesses. However, this species presents a great potential in both aspects: zootechnical and economical. As a result, apparently, the most sustainable productive system would be the extensive one. In order to supply technical subsidies to this system, surveying of populations become necessary. One of the survey methods most used in capybara populations is the direct counting that is usually adopted in ecosystems predominantly herbaceous. However, this methodology relies in some problems. It presents low efficiency in dense forested areas as well as in dealing with fearful capybara individuals. Thus, we proposed in this study a surveying method as an alternative to the direct counting one. The work was done on seven areas (four with closed populations and three open). Weekly, the individuals had been counted, as well as the feces deposited in the period on a sample area, besides getting the real data with respect to fluctuation of the closed populations. The attainment of an index of abundance through the feces counting presented a coefficient of linear regression better that the direct counting, in comparison with the real fluctuation of the population, gotten in closed environments. However, none of the methods presented satisfactory results that they reflected, in the index, the occurred alterations in the population. The feces counting revealed satisfactory to also separate in bands of number of individuals the different populations and in the application to estimate populations based in the technique of Index-manipulation-index. The work raises innumerable questions about the sampling intensity, possible studies about the home range use and the degree of trustworthiness of the surveys based on direct countings.

A capivara é uma espécie da fauna silvestre que se favoreceu da situação de conversão de áreas florestais para fins agropecuários, tornando-se bastante comum. Tal superpopulação causa conflitos, especialmente em virtude de prejuízos agrícolas e riscos de transmissão de doenças. Entretanto, a espécie apresenta grande potencial zootécnico e econômico, sendo que, aparentemente, o sistema produtivo mais sustentável seria o extensivo. Para fornecer subsídios técnicos a este sistema, torna-se necessário o monitoramento das populações. Um dos métodos mais utilizados para populações de capivaras é o de contagem direta dos animais, utilizada usualmente em ambientes mais abertos, porém pouco eficiente em locais de vegetação mais fechada e para populações mais arredias. O que se buscou testar neste trabalho foi um método de monitoramento alternativo à contagem direta. O trabalho foi realizado em sete áreas, sendo quatro com populações fechadas e três abertas. Semanalmente foram contadas as fezes depositadas durante esse período numa área amostral, contados diretamente os animais e levantados dados sobre flutuação real das populações fechadas. A obtenção de um índice de abundância através da contagem de fezes apresentou um coeficiente de regressão linear melhor que a contagem direta, em comparação com a flutuação real da população, obtida em ambientes fechados. Porém, nenhum dos métodos apresentou resultados satisfatórios que refletissem, no índice, as alterações ocorridas na população. A contagem de fezes mostrou-se satisfatória para separar em faixas de número de indivíduos as diferentes populações e também na aplicação da estimativa populacional baseada na técnica de Índice-manipulação-índice. O trabalho levanta inúmeras questões a respeito da intensidade amostral, de possíveis estudos quanto ao uso do habitat e do grau de confiabilidade dos monitoramentos baseados em contagens diretas. / The capybara is a wild species that would be favored by the conversion of the forest areas to farmlands, becoming abundant. Such overpopulation causes conflicts, especially due to agricultural damages and risks of transmission of illnesses. However, this species presents a great potential in both aspects: zootechnical and economical. As a result, apparently, the most sustainable productive system would be the extensive one. In order to supply technical subsidies to this system, surveying of populations become necessary. One of the survey methods most used in capybara populations is the direct counting that is usually adopted in ecosystems predominantly herbaceous. However, this methodology relies in some problems. It presents low efficiency in dense forested areas as well as in dealing with fearful capybara individuals. Thus, we proposed in this study a surveying method as an alternative to the direct counting one. The work was done on seven areas (four with closed populations and three open). Weekly, the individuals had been counted, as well as the feces deposited in the period on a sample area, besides getting the real data with respect to fluctuation of the closed populations. The attainment of an index of abundance through the feces counting presented a coefficient of linear regression better that the direct counting, in comparison with the real fluctuation of the population, gotten in closed environments. However, none of the methods presented satisfactory results that they reflected, in the index, the occurred alterations in the population. The feces counting revealed satisfactory to also separate in bands of number of individuals the different populations and in the application to estimate populations based in the technique of Index-manipulation-index. The work raises innumerable questions about the sampling intensity, possible studies about the home range use and the degree of trustworthiness of the surveys based on direct countings.

<p> The northern fowl mite (<i>Ornithonyssus sylviarum</i>) is an obligate blood-feeding ectoparasite of poultry that can cause decreased egg production, profit loss, anemia, irritation to flocks and personnel, and death to hens in extreme cases. This study aimed to investigate the effects of the northern fowl mite (NFM) on laying hen performance and welfare quality beginning at 17 weeks of age. Two flocks (Trials 1 and 2) involved 800 Tetra Brown hens (n=200 per room) housed in four cage-free rooms at the Purdue University Poultry Unit. Two rooms were infested with NFM and two rooms served as controls. In Trial 1, initial NFM infestation occurred at 24 weeks on 2% (4 hens) in each of the NFM rooms. Because NFM populations were scarce, a second infestation on 2% of hens occurred at 35 weeks. A final attempt to infest with NFM occurred at 41 weeks with all hens in NFM rooms being infested. In Trial 2, initial NFM infestation occurred at 24 weeks on 2% (4 hens) in each of the NFM rooms and a second infestation took place on 2% of hens at 30 weeks of age to boost the NFM population. Egg production and mortality were recorded daily and case weights were recorded weekly. Monthly Welfare Quality® assessments were taken, as well as monthly mite counts on all birds beginning at 28 weeks. Mite checks were conducted periodically on 25% (50 hens) in all rooms between weeks 25 and 38. Data were analyzed in SAS® using the GLM procedure and an ANCOVA and all significant statistical differences were reported at P < 0.05. Proportion of hens with a mite infestation was treated as the covariate. In Trial 1, regardless of treatment, mortality increased dramatically after 21 weeks, leading to a loss of 473 hens by period 7. NFM hen-day production percentage (HD) was approximately 2% lower than the Tetra management guide and control HD was 7% higher than the Tetra management guide. In Trial 1, treatment had an effect on HD, case weights, and feather damage on the belly (P < 0.05). Proportion of hens infested with mites had an effect on percent shell and feather damage on the belly. Cannibalism and pecking in Trial 1 led to extreme feather loss, high mortality, and negatively impacted production parameters. Feather loss and high mortality contributed to the low NFM populations. In Trial 2, percent livability remained high (approximately 97% for both groups) and HD remained slightly lower than the Tetra management guide (9% and 8% lower for control and NFM), respectively. In Trial 2, treatment had an effect on eggs per hen housed, mortality, feather damage on the head and neck, and skin lesions (P < 0.05). Proportion of birds infested with mites had an effect on feather damage on the back, crop, head, and neck (P < 0.05).</p>

<p>The objective of this study was to evaluate the long-term effects that early life events have on heifer growth up to 400 d of age, heifer conception rate, survivability through first lactation, and first lactation milk production of calves raised in automatic calf feeders. Chapter one evaluates possible early life variables that would affect heifer growth and lifetime production as well as research that has been done to predict future growth. The major points discussed include pre-weaning feeding strategies, automatic calf feeding systems, respiratory disease and ways to diagnose cattle with this disease, and the impact of early life growth on the future productivity of the dairy cow.<br></p> <p>The second chapter discusses in detail the process of creating a predictive equation using significant early life variables that affect Holstein heifer growth up to 400 d of age. Variables collected for the growth analysis included sixty d cumulative milk consumption (MC), serum total protein values, respiratory disease and scours incidences, genetic body size, birthweights, and incremental body weight variables on a commercial dairy farm from October 1, 2015 to January 1, 2019. Calves were fed pasteurized whole milk through an automated calf feeding system (feeders = 8) for 60 d (range: 48 – 126d), with a 30% Crude Protein (CP) and 5% Crude Fat enhancer added at 20 g/L of milk. Calves were weighed at birth and several other times prior to calving. Average birth weight of calves was 40.6 ± 4.9 kg (mean ± SD), serum total protein was 6.7 ± 0.63 g/dL, and cumulative 60 d MC was 508.1 ± 67.3 L with a range of 179.9 to 785.1 L. Daily body weights were predicted for individual animals using a third order orthogonal polynomial to model growth curves. The linear and quadratic effects of cumulative 60 d milk consumption, birthweight, feeder, yr born, season born, respiratory incidence, and genetic body size score were significant (<i>P</i><0.0001) when predicting heifer body weight at 400 d (pBW₄₀₀) of age (R²=0.31). There was up to a 263 kg difference in pBW₄₀₀between the heaviest and lightest animal. Birthweight had a significant effect on predicted weights up to 400 d (<i>P</i><0.0001), and for every 1 kg increase in birthweight, there was a 2.5 kg increase in pBW₄₀₀. The quadratic effect of cumulative 60 d MC was significant for pBW₄₀₀ (<i>P</i><0.0001). When 60 d MC was divided into quartiles, heifers had the highest pBW₄₀₀in the third quartile, when 60 d MC was between 507.8 and 552.5 L. Body size composite (genomic index) showed a 21.5 kg difference in pBW₄₀₀ between the top and bottom 25^th percentile of heifers. Heifers were 4.2 kg lighter at 400 d if treated for respiratory disease 3+ times during the first 60 d of life, compared to heifers not treated for respiratory disease.</p> <p>The third chapter utilizes the data described in chapter two and followed those heifers through breeding and first lactation. Heifer conception age and 280 d first lactation milk production (280M) were collected. Average age at conception was 437.5 ± 45.0 d; range of 308 to 631 d (n=5,193), and average 280M was 9,305 ± 1,371.8 kg; range of 712-13,358 kg (n=1,324). Heifer conception age was impacted by season, yr, and the quadratic effects of predicted bodyweight at 300 d of age (pBW₃₀₀) and ADG (0-400; all <i>P</i> < 0.05; total model R² = 0.08). Season born, ADG (0 - 400 d), genomic milk, and the linear effect of heifer conception age had a significant impact on 280M (all <i>P</i> < 0.05; R² = 0.28). For every 1 kg increase in genomic milk value there is 1.42 kg increase in first lactation 280M. Calves not diagnosed with bovine respiratory disease (BRD) from 60-120 d old had a significantly higher chance for survival to first lactation than animals treated three or more times for BRD (hazard ratio = 0.71, 95% CI = 0.574 to 0.886, <i>P </i>= 0.0023, Table 3.3). Heifers treated twice or more for BRD had reduced likelihood to become pregnant than heifers not treated for BRD from 60-120 d (twice <i>P </i>= 0.02; three or more <i>P </i>= 0.05). </p> <p>In conclusion, the results from this thesis support that early life events in Holstein heifers continue to influence future growth and productivity. Future research aims to validate the predictive equation generated in chapter two on farm as well as adapt the equation to other farms allowing them to utilize it as well. The goal is to have farms utilize this tool to aid in their replacement heifer management decisions and to select the most productive heifers for the future of their herds. </p>

<p>Dairy calves in the preweaning period are exposed to a variety of stressors (e.g. disbudding, castration, etc.) and management practices that have the potential to influence their health and productivity later in life. Proper colostrum management at birth is the first step in ensuring calves can reach their full potential in terms of health, growth, and development, while improper management increases a calf’s risk of failed transfer of passive immunity <strong>(FTPI)</strong> which puts the calf at an increased risk of morbidity and mortality. Previous research has indicated there is a difference in colostrum management practices between dairy bull and heifer calves. Due to the marketing of dairy-beef crossbred calves as surplus animals along with dairy bull calves, there is growing interest in the treatment of these calves on farms. The first study presented here (Chapter 2) investigated the relationship between colostrum management practices on 15 farms and the prevalence of FTPI between purebred dairy and dairy-beef crossbred calves on those farms. The results of this study found no influence of calf breed (purebred dairy or dairy-beef crossbred) on the prevalence of FTPI. However, farm tended to influence FTPI. There was also a significant influence of the reported timing of the first colostrum feeding on FTPI, with calves on farms reporting feeding colostrum within 1 hour of birth having decreased odds of experiencing FTPI. In addition to colostrum management at birth, calves are exposed to several management factors during the preweaning period that can cause stressful experiences and result in negative behavioral and physiological outcomes. Early life stress, especially chronic stress, can negatively impact calves later in life. Short term stress load in calves can be quantified by measuring cortisol in the blood serum or saliva; however, these measures are not reflective of chronic stress load because they only measure circulating cortisol. The second study (Chapter 3) considered the efficacy of utilizing hair cortisol concentration <strong>(HCC)</strong> as a measure of stress load in 27 dairy calves exposed to a weekly saline injection or a weekly or biweekly repeated acute stressor (Cosyntropin injection) during the preweaning period. The results revealed no difference in HCC between the treatment groups, though salivary cortisol was increased in calves injected with Cosyntropin. Additionally, calf behavior and growth were not influenced by the treatments in this study. Overall, these studies provided insights into two areas that have not been extensively researched. First, considering dairy-beef crossbred calf management, and second investigating a method to assess chronic stress that has not been extensively researched in calves.</p>

<p>Calves raised in automated milk feeder (AMF) systems benefit from social interaction and having access to large amounts of milk, which they can consume in multiple small meals. Additionally, these systems record longitudinal feeding behavior measurements on each calf. However, if group size, composition, and disease detection are not optimal, the health and performance of calves can be compromised. The analysis of AMF data can provide information that may allow for improved disease detection and group management to maximize health and welfare of pre-weaned dairy calves. A proper understanding of the data generated by AMF and its context are essential to derive meaningful information about health status and group dynamics of dairy calves. Because the goal is that farmers can use this information to support decisions, six years of historical data from a commercial dairy farm were first collected, described, and stored in a research data ecosystem and then used to evaluate feeding and social behavior of calves. The first chapter evaluates the effect of environmental and biological factors on the feeding behavior of 9,737 calves. The results showed that reductions in milk consumption and drinking speed preceded the detection of bovine respiratory disease using farm protocols. In addition to health status, temperature humidity index, birth weight, and parity of the dam also influenced milk consumption and drinking speed. Therefore, including data on the traits of the individuals and the conditions of their environment can improve predictive models for sickness detection and performance assessment. The second chapter evaluates the use of AMF records and social network analysis. Interactions that occur at the autofeeder from 254 calves in five groups were used to rank individual animals and assess the groups’ stability. Enrollment order was associated with dominance rating, based on feeder displacements. Birth weight, however, had no influence on dominance rating. Social network analysis showed that although displacements are not constant over time, calves did not displace every other calf in their group, indicating some selectivity. This study demonstrates the possibility of using longitudinal data from precision technology to assess group dynamics.</p>

<p dir="ltr">The Pekin duck, a major poultry product, is an important livestock species that requires further study to understand their physiological needs and welfare. Welfare improvements can be obtainable by measuring a duck’s response to its environment and developing management practices that allow ducks to explore positive natural behaviors and minimize negative affective states. Assessing welfare includes measuring physical and mental states of an animal and how it copes with its environment. This thesis sets out to use established indicators for mental state, such as serotonin (5-HT) and dopamine (DA), to validate methods of measuring duck affective state applied to environment changes. Affective states can be assessed using neurotransmitter concentrations inserted into turnover equations to understand serotonergic and dopaminergic activity within the synapse. Similarly, gene expression can be linked to affective state by investigating the rate-limiting enzyme in 5-HT and DA synthesis. Developing neuroendocrine profiles for the Pekin duck can elucidate how environmental changes affect physiology and welfare. </p><p dir="ltr">Preening cups are a semi open water source placed within duck barns to improve welfare and allow for positive natural behaviors. Since ducks are waterfowl, many believe these birds need access to open water to develop naturally and have positive welfare. Our lab designed an experiment, referenced in Chapter 3, to compare ducks raised with preening cups to ducks raised with only water nipple lines. At Purdue Animal Science Research and Education Center (ASREC), 260 grow-out Pekin ducks were raised to the industry standard. There were 2 pens that had access to preening cups on day 18 and 2 pens had access to only nipple lines. We collected duck brains on day 18 before preening cup placement (PRE, n = 6). On day 43, we collected duck brains from pens with preening cups (PC, n = 6) and from pens without preening cups (CON, n = 6). Then, brains were hemisected and further dissected into caudal mesencephalon (CM), rostral mesencephalon (RM), diencephalon (DI), and forebrain (FB). The right portions of each brain were used to investigate neurotransmitter concentrations and turnover using mass spectrometry. While the left portions were used to investigate gene expression of tryptophan hydroxylase (TPH1, TPH2) and tyrosine hydroxylase (TH). Our results found no significant differences in 5-HT turnover or 5-HT static levels associated with preening cups across collection days. In the CM, we found a decrease in DA turnovers for PC and CON (p = 0.0067) when compared to PRE. Also, we found a decrease in DA turnover for PC when compared to PRE and CON (p = 0.003) in the RM. In the CM, we found increases in TPH1 expression (p = 0.022) for PC and CON when compared to PRE and in TH expression (p = 0.022) for CON when compared to PRE. There were no significant differences found in the RM and DI brain areas for gene expression. In the FB, we found a decrease in TH gene expression (p = 0.031). Overall, our data highlights an increase in dopaminergic activity within the midbrain. This increase in DA can be correlated with aggressive behavior witnessed from ducks housed with preening cups. Elevated DA is associated with addiction and resource guarding. In this experimental study, we concluded that preening cups placed with a small number of ducks (n = 65 ducks per preening cup) may elicit aggressive behavior and decrease welfare. </p><p dir="ltr">The results of this initial study led us to the question of how a duck affective state is altered by preening cups in a large commercial setting. A commercial Pekin duck barn will place one preening cup for approximately 1,000-1,500 ducks, which means a barn will carry about 3-5 preening cups. Similar methodology was used in Chapter 4 to investigate the ducks affective state using mass spectrometry and qRT-PCR to assess 5-HT and DA activity within the brain. We visited four commercial duck barns with an average of 7,500 ducks on day (d)21 prior to preening cup placement, d28 one week after preening cup placement, and d35 one day prior to processing. We collected litter samples to test moisture content (n = 3/barn/day) and found no differences before or after preening cup placement. We performed a transect walk by moving systematically through each barn and recording the frequency of welfare concerns. All barns showed low percentages of welfare concerns while differences were likely due to natural aging of ducks in a production system. Brains were collected from two locations in the barn including ducks actively using the preening cup (PC) and ducks across the barn not actively performing any behaviors other than standing or sitting (CON). Brains were divided into CM, RM, and DI brain areas and each half was assessed with 5-HT and DA turnover along with TPH1, TPH2, and TH gene expression. No differences were found for 5-HT turnover or static levels. This suggests that preening cups are not altering affective state. DA turnover was decreased in the CM (p < 0.05) and DI (p < 0.001) due to age, but no differences were found between collection location (PC vs CON). We link this increase in dopaminergic activity to natural aging and preparation for puberty as no aggressive behavior was witnessed in commercial barns. Aggression and resource guarding of commercial preening cups is unlikely due to the increased number of ducks per water source and the large space the ducks can access. There was increased TPH1 expression within the RM brain area for d35 ducks when compared to d28 and d21. We conclude that affective state is not variable within the barn based on collection locations. Overall, 5-HT was not affected by preening cups and DA was affected by age. This means that preening cups may not improve affective state and welfare, but they also do not cause determinantal effects either. </p><p dir="ltr">Another major welfare concern associated with environment is transportation for Pekin ducks. To assess how affective state is altered by crating and transportation of hens and drakes, Chapter 5 used similar methodology as the previous studies. Transportation may cause an acutely stressful event while activating a physiological stress response. Chapter 5 measured several central and peripheral physiological parameters to assess responses to transportation. Thirty-six, 23-week-old breeder ducks from a commercial facility were randomly assigned to one of three treatment groups. The control group (CON) was caught and immediate euthanized in the pen, the crate group (CRA) was caught and crated for 90 minutes before euthanasia, and the transport group (TRA) was caught, crated, and loaded into the back of a truck to be driven on country roads at 55 mph for 90 minutes before immediate euthanasia. Blood was collected for corticosterone ELISA analysis and blood smear heterophil to lymphocyte ratio (HLR) analysis. We found that hens showed an increase in HLR (p = 0.035) and serum corticosterone (p = 0.01) due to CRA. Drakes and hens showed an increase in HLR (p = 0.035) and serum corticosterone (p = 0.0084) for TRA. These results suggest that transportation is a stressor that elicits a sex dependent response where hens increase corticosterone and HLR under CRA unlike drakes who only showed a stress response under TRA. Likewise, a sex difference was shown for 5-HT turnover where hens show a stepwise increase from CON to CRA (p = 0.01) and from CRA to TRA (p = 0.016) in the CM and RM. There were no differences for DA turnover while TPH1 gene expression was decreased (p = 0.03) for TRA hens when compared to CON and CRA hens. Our results suggest that transportation negatively shifts affective state by increasing stress responses in ducks and reducing serotonergic activity in hens. In the future, care should be taken to evaluate stress between sexes and minimize transportation time. </p><p dir="ltr">In conclusion, preening cups and transportation are important aspects of a Pekin ducks’ life that alter affective state and physiology. We recommend proper management of preening cups to ensure positive welfare by placing water sources over open pits to prevent excess accumulation of water in the barn. We recommend that while evaluating stressors, researchers need to assess different sexes and collection time from the onset of the stressor. Future studies can include determining affective state for other enrichments such as environmental enrichment devices or investigating commercial barns without preening cups during the production cycle. Continued research could measure affective state following shorter transportation stress or chronic stress to resolve what timeframes alter 5-HT and DA turnover. Transportation may be minimized by installing on-site processing facilities to stun and process animals without transportation to reduce negative affective states. In an academic setting, pharmaceutical intervention may be interesting to investigate to improve affective state during stressful events.</p>

<p>Heart rate variability (<b>HRV</b>), or the variation in time between adjacent heart beats over time, is a non-invasive proxy measure of autonomic nervous system (<b>ANS</b>) function that has been used regularly in studies focused on evaluating livestock stress and welfare. The autonomic nervous system regulates involuntary physiological processes (<i>e.g.</i> respiration and heart rate) and consists of two main components, the parasympathetic (<b>PNS</b>), and sympathetic (<b>SNS</b>) branches, which act to maintain bodily homeostasis (PNS) or stimulate the “fight-or-flight” response after exposure to a stressor (SNS). Traditional linear HRV measures provide an estimation of overall autonomic activity or changes to the balance between the PNS and SNS branches by evaluating changes to the mean, variance, or frequency spectra of the R-R intervals. </p><p>To interpret HRV data obtained via linear HRV measures, particularly spectral HRV analysis, a linear assumption has to be assumed where SNS and PNS activity act in a purely antagonistic manner. However, this assumption is not always met. In many cases, ANS activity is altered in a nonlinear manner, which is reflected to some degree in the variability of heart rate output. Therefore, HRV measures that evaluate nonlinear changes to organizational or structural aspects of the R-R interval variability may be a useful compliment to traditional linear HRV measures for distinguishing between stressed and non-stressed states. The purpose of this dissertation was to evaluate the use of nonlinear HRV measures for evaluating dairy calf disbudding pain, piglet castration pain, growing pig heat stress, and as potential indicators of the subsequent immune response to a lipopolysaccharide (<b>LPS</b>) challenge in growing pigs.</p><p>Chapter 1 provides a knowledge base for understanding HRV and its use as a measure of autonomic stress in studies with livestock species. A brief explanation of animal welfare science, measures used to evaluate an animal’s welfare, and a demonstration of need for non-invasive physiological measures is provided before discussing the physiological basis of HRV. Relevant linear and nonlinear HRV measures are explained and examples of their use in livestock stress research are provided. Finally, a rationale for the studies conducted in this dissertation is presented.</p><p>Chapter 2 evaluates the use of HRV as an indicator of castration pain in 9-d-old piglets over a 3-d experimental period. Compared to sham castrated piglets, surgically castrated piglets exhibited greater low frequency to high frequency ratios (<b>LF/HF</b>), reduced sample entropy (<b>SampEn</b>), and greater percent determinism (<b>ÞT</b>) during the post-castration period. However, postural behavior was not different between treatments and serum cortisol concentrations only tended to differ between treatments at 1 and 24 h post-castration treatment, with surgically castrated pigs having numerically greater serum cortisol concentrations at both timepoints. These results demonstrate the ability of nonlinear HRV measures (SampEn and ÞT) to complement the physiological interpretation of linear HRV measures (LF/HF) in response to castration. Specifically, pigs who were surgically castrated exhibited more regularity (SampEn) and periodicity (ÞT) in their HRV data, and potentially more sympathetic activity (LF/HF) compared to sham castrated piglets, indicating greater pain-related stress. Additionally, HRV was a more sensitive measure of the stress response to castration than readily identifiable behaviors such as posture and the serum cortisol response.</p><p>Chapter 3 evaluates the use of HRV as an indicator of disbudding pain in dairy heifer calves (4 to 7-wk of age) over a 5-d experimental period. Calves who were given lidocaine and meloxicam prior to disbudding exhibited lower mean R-R interval (<b>RR</b>) values and a greater short-term detrended fluctuation analysis scaling exponent (<b>DFAα₁</b>) than sham disbudded calves. Together, these results indicate that calves who received pain mitigation exhibited greater pain-related stress (RR) and reduced physiological complexity in their heart rate signal (DFAα₁). Calves who were disbudded without pain mitigation had an intermediate response compared to sham disbudded calves and calves provided lidocaine and meloxicam. However, their numerical values closely followed those of calves provided lidocaine and meloxicam. These results demonstrate the usefulness of nonlinear HRV measures (DFAα₁) for evaluating nonlinear and correlational aspects of physiological complexity in response to disbudding. Additionally, the HRV results suggest that the provision of meloxicam does not reduce the amount of pain-related stress experienced by calves following disbudding.</p><p>Chapter 4 evaluates the use of HRV as an indicator of heat stress in growing pigs exposed to an acute heat episode. Heat stressed pigs exhibited greater body temperatures and spent less time in an active position compared to thermoneutral control pigs. Additionally, heat stressed pigs displayed an altered nonlinear HRV response to the acute heat phase compared to non-heat stressed control pigs. Specifically, heat stressed pigs exhibited lower SampEn and tended to exhibit greater ÞT, but no alterations to linear measures were observed in response to the acute heat episode. The low frequency to high frequency ratio was higher in heat stressed pigs during the period following the acute heat phase. Therefore, nonlinear HRV measures (particularly SampEn) may be more sensitive to the immediate physiological stress response to increased environmental temperature than traditional linear HRV measures.</p><p>Chapter 5 evaluates the use of baseline HRV as a potential indicator of the subsequent cortisol and pro-inflammatory cytokine response to an LPS challenge in growing pigs. The time for a pig to approach a human (<b>approach time)</b> prior to LPS administration was inversely related to baseline standard deviation of the R-R intervals (<b>SDNN</b>), and directly related to RR and the mean length of diagonal lines in a recurrence plot (<b>Lmean</b>). This result may have implications for the use of HRV as a measure of temperament in livestock species, since pigs with lower baseline SDNN (<i>i.e.</i> greater stress) and greater baseline Lmean (<i>i.e.</i> increased periodicity length in HRV data; greater stress) values took longer to approach a human observer before LPS administration (which occurred 1 d after HRV measurement). Area under the curve values for approach time following LPS administration were inversely related to high frequency spectral power (<b>HF</b>) and directly related to body weight, where pigs with low baseline HF values (<i>i.e. </i>lower parasympathetic activity) and higher body weights were slower to approach a human observer following LPS administration. Additionally, pigs with greater Lmean values had a greater change in body temperature following LPS administration. In conclusion, while baseline HRV measures were not directly representative of the cortisol or cytokine response following an LPS challenge, HF and Lmean may be useful indicators for evaluating certain aspects (sickness behavior and fever) of the innate immune response to an LPS challenge. <b></b></p><p> In conclusion, these studies demonstrate the usefulness of nonlinear HRV measures for evaluating livestock stress. Measures such as sample entropy and those derived from recurrence quantification analysis (ÞT, Lmean) seem to be particularly useful for complementing traditional linear HRV measures and, in some cases, are more sensitive measures of the physiological stress response (see chapter 4). Therefore, their inclusion in future studies on livestock HRV is warranted. However, further work is needed to fully elucidate the physiological significance of nonlinear HRV measures and their response to stress.</p>

When a species is housed in captivity there are facets of the managed environment that can impact on individual and population welfare. A key component of an individual’s environment is its social environment, which can have important implications for animal health and welfare. Highly social species may experience impoverished welfare if kept in captive groups that differ in size, structure and demographic to that experienced by free-living animals. Amongst the most common of social animals to be housed in captivity are the flamingos (Phoenicopteridae). The unique evolutionary biology of these birds means that key aspects of their behaviour depends upon group living. A positive relationship between breeding success and increasing flock size has previously been noted, but how flamingo flocks are structured socially remains mysterious. All six species of flamingo are currently found in captive collections. The three more generalist species, greater (Phoenicopterus roseus), Caribbean (P. ruber) and Chilean (P. chilensis) flamingos are found commonly in zoos and can, under the right conditions, breed well. The other flamingo species are much more specialised in their habitat and dietary requirements and have proved more challenging with regards to their captive management. These three species are the Andean (Phoenicoparrus andinus), James’ (P. jamesi) and lesser (Phoeniconaias minor) flamingos. All six species are included in the experimental work presented in this thesis. This research aimed to evaluate specific elements of flamingo group living using social network analysis (SNA). It also aimed to assess influences of the captive environment (i.e. enclosure style and visitor number) and climate on enclosure usage, time-activity budgets and behavioural diversity to provide, as far as possible, a complete insight into how to measure, assess and evaluate captive flamingo welfare. A synthesis of the relevance of SNA to zoo animal management, and a review of current literature to identify research needs that could evidence good flamingo husbandry form the basis of the first two chapters. These two overview chapters support the questions asked in the following data-based sections of the thesis. Flamingos were observed at WWT Slimbridge Wetland Centre from March 2012 to July 2016 with data on patterns of social associations being collected four times daily (depending upon weather and bird husbandry). Associations were defined as birds within one neck length of each other and, using photos, the affiliations of each bird in the group were recorded. For assessment of bond strength, network position and identification of preferred/avoided partners a Half-Weight Index was applied to these data. Permutation testing was applied to association matrices to determine the difference between the number of observed preferential bonds (and avoided bonds) and Mantel tests were used to compare matrix correlations to assess differences between seasons, species, years and enclosures (where appropriate). The SNA programmes Socprog, UCInet and Netdraw were used to analyse network data. These network data form the basis of three chapters and show that flamingos associate preferentially with non-random bonds occurring in all flocks observed. Influences of social bonds on courtship display were also examined, and temporal changes in association were considered across time, season and year. Finally, to see any influence of animal health on bond preferences, scores of foot condition (used to identify and evaluate the presence and severity of pododermatitis on an individual bird) were analysed alongside of network measures for three flocks of flamingos. To measure enclosure usage, each species’ exhibit was measured and zones accessible to the birds were defined. As exhibit use can be based on resource use (and these resources can form differently-sized areas within an exhibit) a modified Spread of Participation Index (SPI) was used to provide an outcome between 1 (one area or resource used more than others) and 0 (equal use of all resource zones). Time-activity budgets were calculated for all flocks over daytime, and for one flock (measured using remote camera traps) over night. These data are presented in two chapters and demonstrate that captive flamingos can change their activity patterns in a similar manner to that noted in wild birds. Interestingly, flamingos are very active during the night and this provides useful data for zoo personnel to consider when re-assessing husbandry and management plans for these most ubiquitous of zoo birds.